6H8Q | pdb_00006h8q

Structural basis for Scc3-dependent cohesin recruitment to chromatin

• PDB DOI: https://doi.org/10.2210/pdb6H8Q/pdb
• NAKB: 6H8Q

• Classification: CELL CYCLE
• Organism(s): Saccharomyces cerevisiae S288C, Homo sapiens
• Expression System: Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2018-08-03 Released: 2018-08-29 
• Deposition Author(s): Li, Y., Muir, K., Panne, D.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.63 Å
• R-Value Free: 
  0.319 (Depositor), 0.321 (DCC) 
• R-Value Work: 
  0.283 (Depositor), 0.291 (DCC) 
• R-Value Observed: 
  0.285 (Depositor) 

Starting Models: experimental

Literature

Structural basis for Scc3-dependent cohesin recruitment to chromatin.

Li, Y., Muir, K., Bowler, M.W., Metz, J., Haering, C.H., Panne, D.

(2018) Elife 7

• PubMed: 30109982 
• DOI: https://doi.org/10.7554/eLife.38356
• Primary Citation Related Structures: 
  6H8Q


• PubMed Abstract: 
  

  The cohesin ring complex is required for numerous chromosomal transactions including sister chromatid cohesion, DNA damage repair and transcriptional regulation. How cohesin engages its chromatin substrate has remained an unresolved question. We show here, by determining a crystal structure of the budding yeast cohesin HEAT-repeat subunit Scc3 bound to a fragment of the Scc1 kleisin subunit and DNA, that Scc3 and Scc1 form a composite DNA interaction module. The Scc3-Scc1 subcomplex engages double-stranded DNA through a conserved, positively charged surface. We demonstrate that this conserved domain is required for DNA binding by Scc3-Scc1 in vitro, as well as for the enrichment of cohesin on chromosomes and for cell viability. These findings suggest that the Scc3-Scc1 DNA-binding interface plays a central role in the recruitment of cohesin complexes to chromosomes and therefore for cohesin to faithfully execute its functions during cell division.

---

Organizational Affiliation: 
• European Molecular Biology Laboratory, Grenoble, France.
Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, United Kingdom.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 312.81 kDa 
• Atom Count: 16,363 
• Modeled Residue Count: 1,885 
• Deposited Residue Count: 2,576 
• Unique protein chains: 2
• Unique nucleic acid chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cohesin subunit SCC3	A, B	1,150	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: IRR1, SCC3, YIL026C
UniProt
Find proteins for P40541 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P40541  Go to UniProtKB:  P40541

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Sister chromatid cohesion protein 1	C [auth G], D [auth H]	100	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: MCD1, PDS3, RHC21, SCC1, YDL003W, YD8119.04
UniProt
Find proteins for Q12158 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12158  Go to UniProtKB:  Q12158

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*CP*TP*TP*TP*CP*GP*TP*TP*TP*CP*CP*TP*TP*GP*AP*AP*AP*AP*A)-3')	E	19	Homo sapiens

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*CP*TP*TP*TP*CP*GP*TP*TP*TP*CP*CP*TP*TP*GP*AP*AP*AP*AP*A)-3')	F	19	Homo sapiens

Entity ID: 5
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*TP*TP*TP*TP*TP*CP*AP*AP*GP*GP*AP*AP*AP*CP*GP*AP*AP*AP*G)-3')	G [auth C]	19	Homo sapiens

Entity ID: 6
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*CP*TP*TP*TP*CP*GP*TP*TP*TP*CP*CP*TP*TP*GP*AP*AP*AP*AP*A)-3')	H [auth D]	19	Homo sapiens

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.63 Å
• R-Value Free:  0.319 (Depositor), 0.321 (DCC) 
• R-Value Work:  0.283 (Depositor), 0.291 (DCC) 
• R-Value Observed: 0.285 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 296.24	α = 90
b = 110.02	β = 90
c = 115.16	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-08-29 
Deposition Author(s): Li, Y., Muir, K., Panne, D.

Revision History  

• Version 1.0: 2018-08-29
  Type: Initial release
  
• Version 1.1: 2024-01-17
  Changes: Data collection, Database references, Refinement description